Methods of studying soil microbial diversity

Metabolomics Study of Subsurface Wastewater Infiltration System Under Fluctuation of Organic Load

Subsurface Wastewater Infiltration System (SWIS) is a sewage ecological treatment technology with low investment, energy consumption, and operating cost. SWIS soil contains a large variety of microorganisms. The metabolic process and production of microorganisms are an important basis for qualitatively describing the process of pollutant removal. In order to discover the microbial decontamination pathways in SWIS, the metabolic profiles of soil microorganisms in SWIS were analyzed by UPLC-MS. Partial least squares-discriminant analysis (PLS-DA)and principal component analysis (PCA) pattern recognition methods were used to classify the samples. According to the model's variable importance factor (VIP value), potential biomarkers were screened and biological information contained in the metabolites was also analyzed. The correlation between metabolites and environmental factors was explored by RDA analysis. In total, 230 differential metabolites with VIP value greater than 1.5 were screened out when the influent organic load fluctuated at 250 mg L^-1, 400 mg L^-1, and 500 mg L^-1. After identifying and screening, 35 differential metabolites were identified and used to further analyze the metabolic pathway. It turns out that microbial metabolites in SWIS were mainly glycosides, fatty acids, amino acids, pigments, diterpenoids, and some polymers under medium and high organic loading conditions. At low organic load, the microbial metabolites in SWIS were mainly ketones, alcohols, and esters.

Bacterial and Fungal Communities Are Differentially Modified by Melatonin in Agricultural Soils Under Abiotic Stress

An extensive body of evidence from the last decade has indicated that melatonin enhances plant resistance to a range of biotic and abiotic stressors. This has led to an interest in the application of melatonin in agriculture to reduce negative physiological effects from environmental stresses that affect yield and crop quality. However, there are no reports regarding the effects of melatonin on soil microbial communities under abiotic stress, despite the importance of microbes for plant root health and function. Three agricultural soils associated with different land usage histories (pasture, canola or wheat) were placed under abiotic stress by cadmium (100 or 280 mg kg-1 soil) or salt (4 or 7 g kg-1 soil) and treated with melatonin (0.2 and 4 mg kg-1 soil). Automated Ribosomal Intergenic Spacer Analysis (ARISA) was used to generate Operational Taxonomic Units (OTU) for microbial community analysis in each soil. Significant differences in richness (α diversity) and community structures (β diversity) were observed between bacterial and fungal assemblages across all three soils, demonstrating the effect of melatonin on soil microbial communities under abiotic stress. The analysis also indicated that the microbial response to melatonin is governed by the type of soil and history. The effects of melatonin on soil microbes need to be regarded in potential future agricultural applications.

Rapid Characterization and Discovery of Chemical Markers for Discrimination of Xanthii Fructus by Gas Chromatography Coupled to Mass Spectrometry

Xanthii Fructus (XF) is known as a medicinal plant. It has been used as a traditional medicine because of its high biological efficacy. However, there have been few comprehensive studies on the specific chemical composition of the plant and consequently, the information is lacking for the mechanism of the natural product metabolites in humans. In this study, an efficient analytical method to characterize and discriminate two species of Xanthii Fructus (Xanthium canadense Mill. and Xanthium sibiricum Patrin ex Widder) was established. Volatile organic compounds (VOCs), polar metabolites, and fatty acids were classified by integrated sample preparation, which allowed a broad range for the detection of metabolites simultaneously. Gas chromatography-mass spectrometry (GC-MS) followed by a multivariate statistical analysis was employed to characterize the chemical compositions and subsequently to discriminate between the two species. The results demonstrate that the two species possess obviously diverse chemical characteristics of three different classifications, and discriminant analysis was successfully applied to a number of chemical markers that could be used for the discrimination of the two species. Additional quantitative results for the selected chemical markers consistently showed significant differences between the two species.

l-Asparaginase production in rotating bed reactor from Rhizopus microsporus IBBL-2 using immobilized Ca-alginate beads

The present work reports on the production of extracellular l-asparaginase from Rhizopus microsporus IBBL-2 using submerged fermentation (SmF) process free of glutaminase and urease activities. Primary studies done in shake flask showed that the highest l-asparaginase activity of 12.68 U mL^-1 was produced at 72 h with optimized fermentation parameters such as pH 6.0, 4 × 10⁶ fungal cells mL^-1, and agitation of 180 rpm at 30 °C using one-factor-at-a-time (OFAT). Different substrates, nitrogen sources, temperature, pH, the initial number of cells and metal ions were tested to determine the impact on enzyme production. l-Asparaginase activity of 17.68 U mL^-1 was produced after 48 h using immobilized calcium-alginate (Ca-alginate) cells. 4 × 10⁶ cells mL^-1 was entrapped in 3% (W/V) of alginate bead of size 2 mm each at a temperature of 30 °C and pH of 6. The process was optimized using L9 (3⁴) Taguchi Orthogonal Array (OA) technique with a regression coefficient (R ²) value of 0.9709, F value of 33.34 and p value of 0.0025. Scale-up studies involving 200-mL and 1-L rotating bed reactor (RBR) using immobilized beads were done and the results obtained are 20.21 U mL^-1 and 19.13 U mL^-1, respectively, the increased activity with immobilization accounts for reduced shear on cells due to increased stability as compared to the free-flowing cells.

A 16S rDNA PCR-based theoretical to actual delta approach on culturable mock communities revealed severe losses of diversity information

BACKGROUND

Subunits of ribosomal RNA genes (rDNAs) characterized by PCR-based protocols have been the proxy for studies in microbial taxonomy, phylogenetics, evolution and ecology. However, relevant factors have shown to interfere in the experimental outputs in a variety of systems. In this work, a 'theoretical' to 'actual' delta approach was applied to data on culturable mock bacterial communities (MBCs) to study the levels of losses in operational taxonomic units (OTUs) detectability. Computational and lab-bench strategies based on 16S rDNA amplification by 799F and U1492R primers were employed, using a fingerprinting method with highly improved detectability of fragments as a case-study tool. MBCs were of two major types: in silico MBCs, assembled with database-retrieved sequences, and in vitro MBCs, with AluI digestions of PCR data generated from culturable endophytes isolated from cacao trees.

RESULTS

Interfering factors for the 16 s rDNA amplifications, such as the type of template, direct and nested PCR, proportion of chloroplast DNA from a tropical plant source (Virola officinalis), and biased-amplification by the primers resulted in altered bacterial 16S rDNA amplification, both on MBCs and V. officinalis leaf-extracted DNA. For the theoretical data, the maximum number of fragments for in silico and in vitro cuts were not significantly different from each other. Primers' preferences for certain sequences were detected, depending on the MBCs' composition prior to PCR. The results indicated overall losses from 2.3 up to 8.2 times in the number of OTUs detected from actual AluI digestions of MBCs when compared to in silico and in vitro theoretical data.

CONCLUSIONS

Due to all those effects, the final amplification profile of the bacterial community assembled was remarkably simplified when compared to the expected number of detectable fragments known to be present in the MBC. From these findings, the scope of hypotheses generation and conclusions from experiments based on PCR amplifications of bacterial communities was discussed.

Glucose dehydrogenase gene containing phosphobacteria for biofortification of Phosphorus with growth promotion of rice

Phosphorus (P) is an essential plant nutrient, but often limited in soils for plant uptake. A major economic constraint in the rice production is excessive use of chemical fertilizers to meet the P requirement. Bioaugmentation of phosphate solubilizing rhizobacteria (PSB) can be used as promising alternative. In the present study 11 mineral PSB were isolated from Basmati rice growing areas of Pakistan. In broth medium, PSB solubilized tricalcium phosphate (27-354 μg mL^-1) with concomitant decrease in pH up to 3.6 due to the production of different organic acids, predominantly gluconic acid. Of these, 4 strains also have ability to mineralize phytate (245-412 μg mL^-1). Principle component analysis showed that the gluconic acid producing PSB strains (Acinetobacter sp. MR5 and Pseudomonas sp. MR7) have pronounced effect on grain yield (up to 55%), plant P (up to 67%) and soil available P (up to 67%), with 20% reduced fertilization. For simultaneous validation of gluconic acid production by MR5 and MR7 through PCR, new specific primers were designed to amplify gcd, pqqE, pqqC genes responsible for glucose dehydrogenase (gcd) mediated phosphate solubilization. These findings for the first time demonstrated Acinetobacter soli as potent P solubilizer for rice and expands our knowledge about genus specific pqq and gcd primers. These two gcd containing PSB Acinetobacter sp. MR5 (DSM 106631) and Pseudomonas sp. MR7 (DSM 106634) submitted to German culture collection (DSMZ), serve as global valuable pool to significantly increase the P uptake, growth and yield of Basmati rice with decreased dependence on chemical fertilizer in P deficit agricultural soils.

Farmer Reported Pest and Disease Impacts on Root, Tuber, and Banana Crops and Livelihoods in Rwanda and Burundi

Biotic constraints cause major crop losses and, hence, food insecurity in sub-Saharan Africa. This study documented the popularity, production constraints, pests and diseases, farmers’ perceptions on the severity of biotic constraints and the impact of related crop losses on household food security for the key root, tuber and banana (RTB) crops (cassava, potato, sweetpotato and banana). Farmer interviews were conducted in 2014 covering 811 households in Rwanda and Burundi. Farmers were asked to list their RTB crop production constraints, name insect pests and diseases of RTB crops, estimate crop loss due to pests and diseases, and mention if their household experienced any form of food insecurity due to pests and diseases. Cutworms and late blight in potato, banana weevils and banana Xanthomonas wilt in banana, cassava whitefly and cassava mosaic disease in cassava, sweetpotato weevils, and sweetpotato virus disease in sweetpotato were the most predominant pests and diseases reported. Crop losses due to pests and diseases for sweetpotato, banana, potato and cassava were estimated at 26%, 29%, 33%, and 36%, respectively, in Rwanda and 37%, 48%, 38%, and 37% in Burundi. Pests and diseases reduce the profitability of RTB crops, threaten food security, and constitute a disincentive for investment. Sustainable and affordable integrated pest management packages need to be developed.

Sedimentary Marl mudstone as a substrate in a xeric environment revealed by microbiome analysis

The sedimentary Marl mudstone soil is composed primarily of CaCO₃, and is an important pedologic and geomorphologic element known as Marl, extensively dispersed in slopes and ridges in the northern Negev Desert, Israel. The wide Marl soil-layer areas are barren, with well-developed streamsides and no perennial vegetation cover. Soil systems in the Negev Desert have been widely studied, yet very little information was collected on Marl soils, and even less on the microbiome present in the Negev. Thus, an evaluation of the microbial-community inhabitants in a Marl soil layer was conducted in an attempt to distinguish between Marl with surface green mat and bare Marl soil layer. Our objective was to investigate the microbiome and abiotic components of the upper layer (0-5 cm) of Marl and Marl-with-green-mat soil collected in the Negev Desert. Plate-counting enabled the estimation of fungal and bacterial population size, while nested polymerase chain reaction (nPCR) and Ion Torrent sequencing were used to analyze biological diversity. The results indicate significant differences in microbial biomass and microbial-community diversity between Marl and Marl-green mat, despite similar pH levels. Further study is needed to enhance understanding of the activity of the biotic components and their contribution to slope stabilization.

Increasing aridity affects soil archaeal communities by mediating soil niches in semi-arid regions

Soil archaea plays a vital role in the functioning of dryland ecosystems, which are expected to expand and get drier in the future as a result of climate change. However, compared with bacteria and fungi, the impacts of increasing aridity on archaea in these ecosystems remain largely unknown. Here, soil samples were collected along a typical aridity gradient in semi-arid regions in Inner Mongolia, China, to investigate whether and how the increasing aridity affects archaeal communities. The results showed that archaeal richness linearly decreased with increasing aridity. After partialling out the effects of soil properties based on partial least squares regression, the significant aridity-richness relationship vanished. The composition of archaeal communities was distributed according to the aridity gradient. These variations were largely driven by the changes in the relative abundance of Thaumarchaeota, Euryarchaeota and unclassified phyla. Niche-based processes were predominant in structuring the observed archaeal aridity-related pattern. The structural equation models further showed that aridity indirectly reduced archaeal richness through improving soil electrical conductivity (EC) and structured community composition by changing soil total nitrogen (TN). These results suggested that soil salinization and N-losses might be important mechanisms underlying the increasing aridity-induced alterations in archaeal communities, and highlighted the importance of soil niches in mediating the indirect impacts of increasing aridity on archaea.

Long-term effects of untreated wastewater on soil bacterial communities

For 46 years (1957-2002), irrigation with wastewater has increased the amount of heavy metal and organic contaminants in soils and altered bacterial communities in Shenyang, northeastern China. There has been characterization of the different heavy metal and petroleum contaminants in two types of land uses (cornfields and paddy fields). The Nemerow composite indices of heavy metal contaminants have been higher in cornfields (1.17-4.73) than those in paddy fields (0.57-1.64). Molecular-based techniques and biochemical-based techniques were used to analyze soil microbial diversity in our study. The metabolic activity of soil microbe communities was higher in paddy sites than that in cornfields. Organic pollutants such as saturated and polycyclic aromatic hydrocarbons have significantly affected soil bacterial compositions. Heavy metals differed in how they disturbed the microbial communities. Arsenic (As) and lead (Pb) shifted the community composition and decreased microbial diversity; copper (Cu) reduced bacterial abundance in soil; and cadmium (Cd) and chromium (Cr) lowered the metabolic capabilities of bacteria.

Molecular Characterization and Antibiotic Resistance of Foodborne Pathogens in Street-Vended Ready-to-Eat Meat Sold in South Africa

ABSTRACT

The consumption of food contaminated with microbial populations remains a key route of foodborne infection in developing countries and creates a serious public health burden. This study aimed at identifying foodborne pathogens and their antibiotic resistance profiles in ready-to-eat meat sold in public eateries in the Johannesburg area. A total of 115 samples were examined for the incidence of bacteria pathogens and their antibiotic resistance profiles against commonly used antibiotics (ampicillin, tetracycline, chloramphenicol, erythromycin, ciprofloxacin, streptomycin, and sulphonamides) using the molecular and the disc diffusion methods. Fifteen bacteria species were detected in the samples. Staphylococcus aureus had the highest prevalence (25%), and 53.33% of the isolates exhibited multidrug resistance to the antibiotics tested. Among the isolated bacteria, S. aureus; was resistant to at least six antimicrobial agents, whereas 100% of S. aureus,Enterococcus faecalis, and Planomicrobium glaciei were resistant to streptomycin, ciprofloxacin, and chloramphenicol, respectively. This study revealed that a wide diversity of bacteria species contaminate meat sold on the street, which indicates that consumers of ready-to-eat meat sold in public eateries are at risk of food poisoning. Hence, strict intervention strategies should be put in place by government agencies to reduce the menace of food poisoning in the country.

HIGHLIGHTS

RTE meats were analyzed for microbial contamination. Foodborne pathogens were detected in the meat samples. Antibiotic resistance profiles were tested. RTE meats contain foodborne pathogens, and isolates exhibited antibiotic resistance. Consumers of RTE meat in the Johannesburg CBD are at risk of food poisoning.

Toxicity assessment of fresh and weathered petroleum hydrocarbons in contaminated soil- a review

Soil contamination with total petroleum hydrocarbons (TPH) is widespread throughout the globe due to the massive production of TPH anthropogenically and its occurrence in the soil. TPH is toxic to beneficial soil organisms and humans and thus has become a serious concern among the public. Traditionally TPH toxicity in the soil is estimated based on chemical fractions and a range of bioassays including plants, invertebrates and microorganisms. There is a large inconsistency among ecotoxicology data using these assays due to the nature of TPH and their weathering. Therefore, in this article, we critically reviewed the weathered conditions of TPH, the potential fate in soil and the bioindicators for the assessment of the ecotoxicity. Based on the current research and the state-of-the-art problem, we also highlighted key recommendations for future research scope for the real-world solution of the ecotoxicological studies of hydrocarbons.

Physico-chemical and microbial perturbations of Andalusian pine forest soils following a wildfire

Wildfires are a recurrent disturbance in Mediterranean forests, triggered by high fuel load, high environmental temperature and low humidity. Although, human intervention is behind the initiation of most fire episodes, the situation is likely to worsen in the future due to the effects of climate change in the Mediterranean "hot-spot". Here we study chemical, physical and microbial characteristics of burnt soils from two well differentiated sites at Sierra de Cazorla, Segura and Las Villas Natural Park, Andalusia, (Spain) affected and unaffected by a wildfire, and followed their evolution for three years. The soils affected by a severe surface burn showed a significant increase in organic matter after 3years from the fire. Viable bacteria and fungi also increased, especially 2-3years post-burning. Substrate induced respiration (SIR) also increased significantly in burnt soil from site 1 (rendzina on carbonate) while a significant decrease was observed in the burnt soils sampled from site 2 (calcic luvisols) in samples taken one month after the wildfire. A recovery in both SIR and organic matter was observed after 2 and 3years. Of seven soil enzymes studied, only phosphatase activity was significantly higher in most burnt soils over the three years. Analysis of bacterial community diversity using clone libraries showed a recovery in the number of phyla in burnt soils after 2 and 3years in both sites, with an increase in Proteobacteria and Firmicutes and a decrease in Acidobacteria phyla. For Bacteroidetes, the percentages were lower in most burnt samples. This study reveals that if wildfire increases the organic matter availability, then the microbial community responds with increased activity and biomass production. Although fire exerts an initial impact on the soil bacterial community, its structure and functional profile soon recovers (after 2-3years) contributing to soil recovery.

Novel insights in biopurification system for dissipation of a pesticide mixture in repeated applications

A biopurification system based on the adsorption and degradation capacity of a biomixture to degrade a mixture of pesticides (atrazine, chlorpyrifos, iprodione; 50 mg kg^-1 each) in repeated applications (0, 30, and 60 days) was evaluated. Tanks of 1 m³ packed with a biomixture (ρ 0.29 g mL^-1) with and without vegetal cover were used. The biomixture contained soil, peat, and wheat straw in a proportion 1:1:2 by volume, respectively. Pesticide concentrations, biological activities (urease, phenoloxidase, and dehydrogenase), and microbial community changes (DGGE and qPCR) were evaluated periodically. Pesticide dissipation was higher in tanks with vegetal cover (> 95%) and no variation was observed after the three applications; contrarily, pesticide dissipation decreased in the tank without vegetal cover after each application. The presence of vegetal cover decreased the half-life of pesticides by at least twice. Biological activities were in general not affected by the application and reapplication of pesticides in the same treatment; however, they exhibited some differences between tanks containing and lacking the vegetal cover. High similarity between microbial groups (actinobacteria, bacteria, and fungi) was observed, suggesting no influence ascribable to the successive pesticide applications. The number of copies of bacteria and actinobacteria remained almost constant during the assay. However, the number of copies of fungi was significantly higher in the uncontaminated tank without vegetal cover.

Plant Species and Heavy Metals Affect Biodiversity of Microbial Communities Associated With Metal-Tolerant Plants in Metalliferous Soils

We here assess the biodiversity of the rhizosphere microbial communities of metal-tolerant plant species Arabidopsis arenosa, Arabidopsis halleri, Deschampsia caespitosa, and Silene vulgaris when growing on various heavy metal polluted sites. Our broad-spectrum analyses included counts for total and metal-tolerant culturable bacteria, assessments of microbial community structure by phospholipid fatty acid (PLFA) profiling and community-level analysis based on BIOLOG-CLPP to indicate functional diversity. The genetic-biochemical diversity was also measured by denaturing gradient gel electrophoresis (PCR-DGGE) and metabolomic analysis (HPLC-MS). Different rhizospheres showed distinctive profiles of microbial traits, which also differed significantly from bulk soil, indicating an influence from sampling site as well as plant species. However, total bacterial counts and PCR-DGGE profiles were most affected by the plants, whereas sampling site-connected variability was predominant for the PLFA profiles and an interaction of both factors for BIOLOG-CLPP. Correlations were also observed between pH, total and bioavailable Cd or Zn and measured microbial traits. Thus, both plant species and heavy-metals were shown to be major determinants of microbial community structure and function.

Selection and evaluation of microorganisms for biodegradation of agricultural plastic film

Three Bacillus amyloliquefaciens isolates (HK1, GSDM02, and GSDM15) were tested for effectiveness in biodegradation of plastic films. Isolates were screened by plate on carbon-free medium and by using the clear-zone formation test. Their biodegradation ability was analyzed based on: film weight reduction, pH change of the fluid medium, a soil microbial biomass carbon test, scanning electron microscopy (SEM), and Fourier transform infrared spectrometry (FTIR). Polyvinyl alcohol (PVA) clear-zone and film weight reduction results revealed that the strain with a bigger clear-zone had a better biodegradation effect, that PVA can be evenly distributed in the medium, and that PVA can be a substitution for polyethylene in screening the biodegradation of strains. SEM and FTIR revealed that HK1 can tear the film apart and make surface chemical changes within 30 days. HK1 exhibited a better biodegradation effect in all tests, indicating its potential for helping solve the plastic pollution problems.

Effects of a vegetable-eel-earthworm integrated planting and breeding system on bacterial community structure in vegetable fields

Agricultural production combined with planting and breeding, which can reduce chemical fertilizer and pesticide applications, reduce losses due to natural disasters, and improve the output and quality of agricultural products, is an important way to achieve green, circular and efficient production. To assess effects on soil bacterial community structure, a vegetable-eel-earthworm integrated planting and breeding platform (VEE-IPBP) combined with experiment planting was established at Chongming Island, Shanghai and compared to traditional planting. High-throughput sequencing to reveal soil bacterial community structure was performed on samples collected at 0, 3 and 6 years after implementation of the two models. Over time, the Shannon index first increased and then decreased in the VEE-IPBP system and was reduced by 3.2% compared to the traditional planting (In the same time and space scale, the single-degree planting method of dryland vegetables under mechanical cultivation is adopted) (p < 0.05). In contrast, Chao and Ace indices were increased by 2.4% and 3.2%. Thus, soil bacterial diversity was markedly different in the two planting models. The abundance of Proteus, Cyanophyta and Cyanophyta in soil increased after 6 years, and the proportion of Lysinibacillus increased significantly, contributing to improvement in soil disease resistance. Redundancy analysis (RDA) showed that the soil pH and water content were the main factors influencing the change in soil bacterial community structure in the two planting models, and the dominant species of soil bacteria were Lysobacter and Bacillus.

Characterization of bacterial community structure in a hydrocarbon-contaminated tropical African soil

The bacterial community structure in a hydrocarbon-contaminated Mechanical Engineering Workshop (MWO) soil was deciphered using 16S rRNA gene clone library analysis. Four hundred and thirty-seven clones cutting across 13 bacterial phyla were recovered from the soil. The representative bacterial phyla identified from MWO soil are Proteobacteria, Bacteroidetes, Chloroflexi, Acidobacteria, Firmicutes, Actinobacteria, Verrucomicrobia, Planctomycetes, Ignavibacteriae, Spirochaetes, Chlamydiae, Candidatus Saccharibacteria and Parcubacteria. Proteobacteria is preponderant in the contaminated soil (51.2%) with all classes except Epsilonproteobacteria duly represented. Rarefaction analysis indicates 42%, 52% and 77% of the clone library is covered at the species, genus and family/class delineations with Shannon diversity (H') and Chao1 richness indices of 5.59 and 1126, respectively. A sizeable number of bacterial phylotypes in the clone library shared high similarities with strains previously described to be involved in hydrocarbon biodegradation. Novel uncultured genera were identified that have not been previously reported from tropical African soil to be associated with natural attenuation of hydrocarbon pollutants. This study establishes the involvement of a wide array of physiologically diverse bacterial groups in natural attenuation of hydrocarbon pollutants in soil.

Soil bacterial community response to vegetation succession after fencing in the grassland of China

Natural succession is an important process in terrestrial system, playing an important role in enhancing soil quality and plant diversity. Soil bacteria is the linkage between soil and plant, has an important role in aboveground community dynamics and ecosystem functioning in terrestrial ecosystems, driving the decomposition of soil organic matter and plant litter. However, the role of soil bacteria in the secondary succession has not been well understood, particularly in the degraded soil of Loess Plateau. In this study, we investigated soil nutrients and soil bacterial community during the secondary succession after a long-term fencing in the grassland, in the Yuwu Mountain, northwest China. The chronosequence included 1year, 12years, 20years and 30years. The soil bacterial community composition was determined by the Illumina HiSeq sequencing method. The data showed that soil bacterial diversity had no significant changes along the chronosequence, but soil bacterial community compositions significantly changed. Proteobacteria, Acidobacteria and Actinobacteria were the main phyla in all the samples across succession. With the accumulation of soil organic matter and nutrients, the relative abundance of Actinobacteria decreased, whereas Proteobacteria increased. These shifts may be caused by the increase of the available nutrients across the secondary succession. In the younger sites, soils were dominated by oligotrophic groups, whereas soil in the late-succession site were dominated by copiotrophic groups, indicating the dependence of soil bacterial community composition on the contents of soil available nutrients.

Isolation, identification and anti-candidal activity of filamentous fungi from Saudi Arabia soil

Ten fungal strains; namely, Penicillium melinii, Petriella setifera, Aspergillus pseudo-niger, Alternaria chlamydospora, Pythium nayoroense, Phoma glomerata, Mucor ramosissimus, Mucor racemosus, Fusarium chlamydosporum and Rhizopus azygosporus were isolated from soil. The extra- and intra-cellular extracts of the fungal strains grown on malt extract and yeast-extract sucrose media were screened for their anticandidal activity against different clinically-isolated Candida species. Most of the fungal extracts showed activity against different Candida species. However, the fungal strains grew on malt extract showed greater activities than those grew on yeast extract sucrose media. The activity of the intracellular was higher than the extracellular metabolites. All fungal extracts (extra and intra) were similar in chemical constituent; they contained carbohydrates and/or glycosides, unsaturated sterols and/or triterpens, tannins and traces of coumarins. Alkaloids, flavonoids, saponins, anthraquinones and cardenolides were no detected. The intra-cellular extracts contained more compounds than the extra-cellular extracts.

Usefulness and limitations of sample pooling for environmental DNA metabarcoding of freshwater fish communities

Environmental DNA (eDNA) metabarcoding has been used increasingly to assess biodiversity of aquatic vertebrates. However, there still remains to be developed a sampling design of eDNA metabarcoding that can ensure high detection rates of species with minimum total survey effort, especially for large-scale surveys of aquatic organisms. We here tested whether pooling of eDNA samples can be used to evaluate biodiversity of freshwater fishes in four satellite lakes of Lake Biwa, Japan. Fish communities detected by eDNA metabarcoding of the mitochondrial 12S region were compared between the individual and pooled samples. In the individual samples, 31, 22, 33, and 31 fish lineages (proxies for species) were observed at the respective sites, within which moderate spatial autocorrelation existed. In the pooled samples, 30, 20, 29, and 27, lineages were detected, respectively, even after 15 PCR replicates. Lineages accounting for < 0.05% of the total read count of each site’s individual samples were mostly undetectable in the pooled samples. Moreover, fish communities detected were similar among PCR replicates in the pooled samples. Because of the decreased detection rates, the pooling strategy is unsuitable for estimating fish species richness. However, this procedure is useful potentially for among-site comparison of representative fish communities.

A novel baiting microcosm approach used to identify the bacterial community associated with Penicillium bilaii hyphae in soil

It is important to identify and recover bacteria associating with fungi under natural soil conditions to enable eco-physiological studies, and to facilitate the use of bacterial-fungal consortia in environmental biotechnology. We have developed a novel type of baiting microcosm, where fungal hyphae interact with bacteria under close-to-natural soil conditions; an advantage compared to model systems that determine fungal influences on bacterial communities in laboratory media. In the current approach, the hyphae are placed on a solid support, which enables the recovery of hyphae with associated bacteria in contrast to model systems that compare bulk soil and mycosphere soil. We used the baiting microcosm approach to determine, for the first time, the composition of the bacterial community associating in the soil with hyphae of the phosphate-solubilizer, Penicillium bilaii. By applying a cultivation-independent 16S rRNA gene-targeted amplicon sequencing approach, we found a hypha-associated bacterial community with low diversity compared to the bulk soil community and exhibiting massive dominance of Burkholderia OTUs. Burkholderia is known be abundant in soil environments affected by fungi, but the discovery of this massive dominance among bacteria firmly associating with hyphae in soil is novel and made possible by the current bait approach.

Diversity and dynamics of the DNA- and cDNA-derived compost fungal communities throughout the commercial cultivation process for Agaricus bisporus

Commercial cultivation of the button mushroom Agaricus bisporus is performed through the inoculation of a semipasteurized composted material. Pasteurization of the compost material prior to inoculation results in a substrate with a fungal community that becomes dominated by A. bisporus. However, little is known about the composition and activity in the wider fungal community beyond the presence of A. bisporus in compost throughout the mushroom cropping process. In this study, the fungal cropping compost community was characterized by sequencing nuc rDNA ITS1-5.8S-ITS2 amplified from extractable DNA and RNA. The fungal community generated from DNA extracts identified a diverse community containing 211 unique species, although only 51 were identified from cDNA. Agaricus bisporus was found to dominate in the DNA-derived fungal community for the duration of the cropping process. However, analysis of cDNA extracts found A. bisporus to dominate only up to the first crop flush, after which activity decreased sharply and a much broader fungal community became active. This study has highlighted the diverse fungal community that is present in mushroom compost during cropping.

Congolese Rhizospheric Soils as a Rich Source of New Plant Growth-Promoting Endophytic Piriformospora Isolates

In the last decade, there has been an increasing focus on the implementation of plant growth-promoting (PGP) organisms as a sustainable option to compensate for poor soil fertility conditions in developing countries. Trap systems were used in an effort to isolate PGP fungi from rhizospheric soil samples collected in the region around Kisangani in the Democratic Republic of Congo. With sudangrass as a host, a highly conducive environment was created for sebacinalean chlamydospore formation inside the plant roots resulting in a collection of 51 axenically cultured isolates of the elusive genus Piriformospora (recently transferred to the genus Serendipita). Based on morphological data, ISSR fingerprinting profiles and marker gene sequences, we propose that these isolates together with Piriformospora williamsii constitute a species complex designated Piriformospora (= Serendipita) 'williamsii.' A selection of isolates strongly promoted plant growth of in vitro inoculated Arabidopsis seedlings, which was evidenced by an increase in shoot fresh weight and a strong stimulation of lateral root formation. This isolate collection provides unprecedented opportunities for fundamental as well as translational research on the Serendipitaceae, a family of fungal endophytes in full expansion.

Assessment of species richness in Lake Dal, Kashmir, based on classical approach, physiological approach and rDNA ITS sequences from isolates

As a first description to document the species richness in Dal Lake, a freshwater lake ecosystem in Kashmir valley, an extensive network of sixteen sampling stations with distinguishing features was sampled seasonally for two years. The identification process yielded fifty-one species probably first and new records for this area to date. The taxonomic groups observed were those with species from Ascomycetes (inclusive of yeasts), Basidiomycetes, Blastocladiomycetes, Zygomycetes, and Peronosporomycetes. Each phylum was represented by a single Order, with the exception of the Peronosporomycetes, which was represented by two Orders- Saprolegniales and Pythiales. In the filamentous fungal group, family Trichocomaceae was dominant followed by Saccharomycetaceae, Mucoraceae, Nectriaceae, Tremellaceae and Hypocreaceae. However, in the group of zoosporic & fungal like eukaryotes, family Saprolegniaceae was most dominant followed by Blastocladiaceae and Pythiaceae. A dramatic decrease in fungal load was observed in different seasons with highest colonial load in the summer season and lowest in the winter season. The observed distribution was statistically significant for both the filamentous fungal species (p < 0.01) as well as zoosporic fungi & fungal like eukaryotes (p < 0.05). In order to assess biodiversity patterns of fungi more accurately, it is necessary to repeat such investigations in other areas and to improve the tools for taxonomic identification of these highly diverse but mostly microscopic organisms.

Extremely Acidic Soils are Dominated by Species-Poor and Highly Specific Fungal Communities

Highly acidic soils (pH < 3) represent an environment which might potentially offer new biotechnologically interesting fungi. Nevertheless, only little data on fungal communities in highly acidic habitats are available. Here, we focused on the diversity of cultivable filamentous microfungi in highly acidic soils (pH < 3) in the Czech Republic. Altogether, 16 soil samples were collected from four sampling sites and were processed by various approaches. In total, 54 fungal taxa were isolated and identified using classical as well as molecular markers. All dominant species were found both as living mycelia and as resistant stages. Numerous recently described or unknown taxa were isolated. The core of the fungal assemblage under study consisted of phylogenetically unrelated and often globally distributed fungi exclusively inhabiting highly acidic habitats like Acidiella bohemica, Acidomyces acidophilus, and unidentified helotialean fungus, as well as taxa known from less acidic and often extreme environments like Acidea extrema, Penicillium simplicissimum s.l., and Penicillium spinulosum. The large number of identified specialized species indicates that highly acidic environments provide suitable conditions for the evolution of specialist species. The occurrence of ubiquitous fungi in highly acidic substrates points to the principal role of competition in the colonization of such environments. The detected taxa did not require low pH to survive, because they can grow in a broad range of pH.

Impact of fertilization by natural manure on the microbial quality of soil: Molecular approach

The quality of soil is strongly bound by several interactions between chemical and biological components, including microbial composition, which are a key importance for soil performance. Cultural activities have a huge induction on soil health, through both modification of physicochemical proprieties and changing on soil microbial communities. This usually affects the safety of soil, and then the crop production and water.

In the present work, the information on bacterial community composition was determined from a set of 6 soils collected from 2 farms in agricultural land of Marrakech (Morocco), one of which used poultry manure (PM) and the other cow manure (CM) as fertilizers. To profile this structure of the bacterial community Denaturing Gradient Gel Electrophoresis (DGGE) of 16S rDNA fragments has been used.

These amendments resulted in the appearance of several novel bands and different relative intensities of bands between the control station and other sites studied. The stations most affected are those receiving a supply of manure rather high, which results in an organic and bacterial load in the soil. The results showed a bacterial diversity very important indicating a fecal contamination like Bacteroides, Pseudomonas, Staphylococcus,… etc. Bacteria pertain to the phylum Firmicutes and Bacteroidetes were noted to be the dominant ribotype in amended soil.

Moreover, this work demonstrates also the existence of pathogens strains in soil amended by poultry manure (PM) belonging to the Clostridiales order and Pseudomonadales. The pathogenic bacteria detected posing a hazard of human contagion when they are used for soil practice.

Insight of Proteomics and Genomics in Environmental Bioremediation

Bioremediation of hazardous substances from environment is a major human and environmental health concern but can be managed by the microorganism due to their variety of properties that can effectively change the complexity. Microorganisms convey endogenous genetic, biochemical and physiological assets that make them superlative proxies for pollutant remediation in habitat. But, the crucial step is to degrade the complex ring structured pollutants. Interestingly, the integration of genomics and proteomics technologies that allow us to use or alter the genes and proteins of interest in a given microorganism towards a cell-free bioremediation approach. Resultantly, efforts have been finished by developing the genetically modified (Gm) microbes for the remediation of ecological contaminants. Gm microorganisms mediated bioremediation can affect the solubility, bioavailability and mobility of complex hazardous.

Impact assessment of silver nanoparticles on plant growth and soil bacterial diversity

The present study was carried out to investigate the impact of silver nanoparticles (AgNPs) on the growth of three different crop species, wheat (Triticum aestivum, var. UP2338), cowpea (Vigna sinensis, var. Pusa Komal), and Brassica (Brassica juncea, var. Pusa Jai Kisan), along with their impact on the rhizospheric bacterial diversity. Three different concentrations (0, 50 and 75 ppm) of AgNPs were applied through foliar spray. After harvesting, shoot and root parameters were compared, and it was observed that wheat was relatively unaffected by all AgNP treatments. The optimum growth promotion and increased root nodulation were observed at 50 ppm treatment in cowpea, while improved shoot parameters were recorded at 75 ppm in Brassica. To observe the impact of AgNPs on soil bacterial community, sampling was carried out from the rhizosphere of these crops at 20 and 40 days after the spraying of AgNPS. The bacterial diversity of these samples was analyzed by both cultural and molecular techniques (denaturing gradient gel electrophoresis). It is clearly evident from the results that application of AgNPs changes the soil bacterial diversity and this is further influenced by the plant species grown in that soil. Also, the functional bacterial diversity differed with different concentrations of AgNPs.

Soil contamination with olive mill wastes negatively affects microbial communities, invertebrates and plants

The aim of the present study was to evaluate the ecotoxicological effects of olive mill waste (OMW) on soil habitat function. To this end, soil samples from OMW evaporating ponds (S1-S5) located at Agareb (Sfax, Tunisia) and a reference soil (R) were collected. The effects of OMW on the springtails Folsomia candida (F.c.), the earthworm species Eisenia fetida (E.f.), Enchytraeus crypticus (E.c.) reproduction and on the soil living microbial communities were investigated. E.f. reproduction and tomato growth assays were performed in the reference soil amended with 0.43 to 7.60 % (w_OMW/w_ref-soil) mass ratios of dried OMW. Changes in microbial function diversity were explored using sole-carbon-source utilization profiles (BiologEcoPlates^®). E.f. absolutely avoided (100 %) the most polluted soil (S4) while the F.c. moderately avoided (37.5 ± 7.5 %) the same soil. E.c. reproduction in S4 was significantly lower than in S1, S2, S3 and S5, and was the highest in R soil. Estimated effect concentration EC₅₀ for juveniles' production by E.f., and for tomato fresh weight and chlorophyll content were 0.138, 0.6 and 1.13 %, respectively. Community level physiological profiles (CLPPs) were remarkably different in R and S4 and a higher similarity was observed between soils S1, S2, S3 and S5. Principal component analysis (PCA) revealed that differences between soil microbial functional diversity were mainly due to high polyphenol concentrations, while the salinity negatively affected E.c. reproduction in OMW contaminated soils. These results clearly reflect the high toxicity of dried OMW when added to agricultural soils, causing severe threats to terrestrial ecosystem functions and services provided by invertebrates and microbial communities.

Optimization of Xylanase Production through Response Surface Methodology by Fusarium sp. BVKT R2 Isolated from Forest Soil and Its Application in Saccharification

Xylanses are hydrolytic enzymes with wide applications in several industries like biofuels, paper and pulp, deinking, food, and feed. The present study was aimed at hitting at high yield xylanase producing fungi from natural resources. Two highest xylanase producing fungal isolates-Q12 and L1 were picked from collection of 450 fungal cultures for the utilization of xylan. These fungal isolates-Q12 and L1 were identified basing on ITS gene sequencing analysis as Fusarium sp. BVKT R2 (KT119615) and Fusarium strain BRR R6 (KT119619), respectively with construction of phylogenetic trees. Fusarium sp. BVKT R2 was further optimized for maximum xylanase production and the interaction effects between variables on production of xylanase were studied through response surface methodology. The optimal conditions for maximal production of xylanase were sorbitol 1.5%, yeast extract 1.5%, pH of 5.0, Temperature of 32.5°C, and agitation of 175 rpm. Under optimal conditions, the yields of xylanase production by Fusarium sp. BVKT R2 was as high as 4560 U/ml in SmF. Incubation of different lignocellulosic biomasses with crude enzyme of Fusarium sp. BVKT R2 at 37°C for 72 h could achieve about 45% saccharification. The results suggest that Fusarium sp. BVKT R2 has potential applications in saccharification process of biomass.

Pyrosequencing analysis revealed complex endogenetic microorganism community from natural DongChong XiaCao and its microhabitat

BACKGROUND

Ophiocordyceps sinensis (DongChong XiaCao (DCXC) in Chinese), a fungal parasite of caterpillars, is a traditional Chinese medicine. Bioactive components isolated from natural DCXC possess a wide range of pharmacological actions. Many efforts have been directed towards isolating the fungi based on culture-dependent methods for investigation of fungal diversity in order to determine the anamorph of natural DCXC and find new medicinal fungi resources, and the results have been varied.

RESULTS

In the present study, a total of 44,588 bacterial and 51,584 fungal sequences corresponding to 11,694 and 9297 putative operational taxonomic units (OTU) were respectively identified by a Roche/454-based, high throughput sequence analysis of 16S rRNA genes and ITS regions. The main bacterial groups were Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria and Firmicutes, while the Ascomycota, Basidiomycota and Zygomycota were the main fungal phyla. Proteobacteria presented 68.4, 49.5, 38.9 and 35.6 % of all bacteria in the sclerotia, stromata, external mycelial cortices and soil, respectively. As the main fungi phyla, Ascomycota presented 21.0, 45.6 26.4 and 59.3 % in the sclerotia, stromata, external mycelial cortices and soil, respectively. Bacterial and fungal communities were more diverse in the environmental sample than in the natural DCXC sample. Microbial communities were obviously distinct in each sample. Several novel unclassifiable bacterial (10.41 %) and fungal (37.92 %) species were also detected.

CONCLUSIONS

This study revealed an abundant endogenetic fungal and bacterial resources and a variety of genetic information in natural DCXC by high-throughput 454 sequencing technology. Microorganism that had been discovered in natural DCXC will provide sources for screening the new bioactive metabolites and its biotechnological application.

Relationship between microbial community dynamics and process performance during thermophilic sludge bioleaching

Heavy metals can be removed from the sludge using bioleaching technologies at thermophilic condition, thereby providing an option for biotreatment of wasted sludge generated from wastewater treatment. The purposes of this study were to establish a molecular biology technique, real-time PCR, for the detection and enumeration of the sulfur-oxidizing bacteria during the thermophilic sludge bioleaching. The 16S rRNA gene for real-time PCR quantification targeted the bioleaching bacteria: Sulfobacillus thermosulfidooxidans, Sulfobacillus acidophilus, and Acidithiobacillus caldus. The specificity and stringency for thermophilic sulfur-oxidizing bacteria were tested before the experiments of monitoring the bacterial community, bacterial number during the thermophilic sludge bioleaching and the future application on testing various environmental samples. The results showed that S. acidophilus was identified as the dominant sulfur-oxidizing bacteria, while A. caldus and S. thermosulfidooxidans occurred in relatively low numbers. The total number of the sulfur-oxidizing bacteria increased during the thermophilic bioleaching process. Meanwhile, the decrease of pH, production of sulfate, degradation of SS/VSS, and solubilization of heavy metal were found to correlate well with the population of thermophilic sulfur-oxidizing bacteria during the bioleaching process. The real-time PCR used in this study is a suitable method to monitor numbers of thermophilic sulfur-oxidizing bacteria during the bioleaching process.

Abundance and Diversity of Bacterial, Archaeal, and Fungal Communities Along an Altitudinal Gradient in Alpine Forest Soils: What Are the Driving Factors?

Shifts in soil microbial communities over altitudinal gradients and the driving factors are poorly studied. Their elucidation is indispensable to gain a comprehensive understanding of the response of ecosystems to global climate change. Here, we investigated soil archaeal, bacterial, and fungal communities at four Alpine forest sites representing a climosequence, over an altitudinal gradient from 545 to 2000 m above sea level (asl), regarding abundance and diversity by using qPCR and Illumina sequencing, respectively. Archaeal community was dominated by Thaumarchaeota, and no significant shifts were detected in abundance or community composition with altitude. The relative bacterial abundance increased at higher altitudes, which was related to increasing levels of soil organic matter and nutrients with altitude. Shifts in bacterial richness and diversity as well as community structure (comprised basically of Proteobacteria, Acidobacteria, Actinobacteria, and Bacteroidetes) significantly correlated with several environmental and soil chemical factors, especially soil pH. The site at the lowest altitude harbored the highest bacterial richness and diversity, although richness/diversity community properties did not show a monotonic decrease along the gradient. The relative size of fungal community also increased with altitude and its composition comprised Ascomycota, Basidiomycota, and Zygomycota. Changes in fungal richness/diversity and community structure were mainly governed by pH and C/N, respectively. The variation of the predominant bacterial and fungal classes over the altitudinal gradient was the result of the environmental and soil chemical factors prevailing at each site.

Improved lysis of single bacterial cells by a modified alkaline-thermal shock procedure

Single-cell genomics (SCG) is a recently developed tool to study the genomes of unculturable bacterial species. SCG relies on multiple-strand displacement amplification (MDA), PCR, and next-generation sequencing (NGS); however, obtaining sufficient amounts of high-quality DNA from samples is a major challenge when performing this technique. Here we present an improved bacterial cell lysing procedure that combines incubation in an alkaline buffer with a thermal shock (freezing/heating) treatment to yield highly intact genomic DNA with high efficiency. This procedure is more efficient in lysing Bacillus subtilis and Synechocystis cells compared with two other frequently used lysis methods. Furthermore, 16S ribosomal RNA gene and overall genome recovery were found to be improved by this method using single cells from a Utah desert soil community or Escherichia coli single cells, respectively. The efficiency of genome recovery for E. coli single cells using our procedure is comparable with that of the REPLI-g Single Cell (sc) Kit, but our method is much more economical. By providing high-quality genome templates suitable for downstream applications, our procedure will be a promising improvement for SCG research.

Nicosulfuron application in agricultural soils drives the selection towards NS-tolerant microorganisms harboring various levels of sensitivity to nicosulfuron

The action mode of sulfonylurea herbicides is the inhibition of the acetohydroxyacid synthase (AHAS) required for the biosynthesis of amino acids valine and isoleucine in plants. However, this enzyme is also present in a range of non-targeted organisms, among which soil microorganisms are known for their pivotal role in ecosystem functioning. In order to assess microbial toxicity of sulfonylurea herbicide nicosulfuron (NS), a tiered microcosm (Tier I) to field (Tier II) experiment was designed. Soil bacteria harboring AHAS enzyme tolerant to the herbicide nicosulfuron were enumerated, isolated, taxonomically identified, and physiologically characterized. Results suggested that application of nicosulfuron drives the selection towards NS-tolerant bacteria, with increasing levels of exposure inducing an increase in their abundance and diversity in soil. Tolerance to nicosulfuron was shown to be widespread among the microbial community with various bacteria belonging to Firmicutes (Bacillus) and Actinobacteria (Arthrobacter) phyla representing most abundant and diverse clusters. While Arthrobacter bacterial population dominated community evolved under lower (Tier II) nicosulfuron selection pressure, it turns out that Bacillus dominated community evolved under higher (Tier I) nicosulfuron selection pressure. Different NS-tolerant bacteria likewise showed different levels of sensitivity to the nicosulfuron estimated by growth kinetics on nicosulfuron. As evident, Tier I exposure allowed selection of populations able to better cope with nicosulfuron. One could propose that sulfonylureas-tolerant bacterial community could constitute a useful bioindicator of exposure to these herbicides for assessing their ecotoxicity towards soil microorganisms.